Variant report

Variant	rs12410866
Chromosome Location	chr1:160108803-160108804
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160104302..160107204-chr1:160107299..160108872,2	MCF-7	breast:
2	chr1:160093121..160095812-chr1:160107178..160109878,2	K562	blood:

Variant related genes	Relation type
ENSG00000018625	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11265328	0.84[AMR][1000 genomes]
rs1131891	1.00[ASW][hapmap]
rs12402134	0.84[AMR][1000 genomes]
rs12407381	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12408200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12410580	1.00[MKK][hapmap]
rs17368402	1.00[MKK][hapmap]
rs17846705	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17846715	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17846717	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17846718	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2070701	1.00[JPT][hapmap]
rs3761684	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes]
rs41288127	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4656879	0.85[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs55843060	0.87[EUR][1000 genomes]
rs55845795	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55884181	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56003400	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56022217	0.89[EUR][1000 genomes]
rs56287743	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs911229	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3327316	chr1:159985477-160151281	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv1794281	chr1:160029416-160111565	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv1820784	chr1:160029416-160159395	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv534165	chr1:160029416-160187302	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv872490	chr1:160083012-160121488	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv3453724	chr1:160098374-160136495	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	esv3453725	chr1:160098456-160136351	Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12410866	CASQ1	cis	parietal	SCAN
rs12410866	ZBTB7B	cis	cerebellum	SCAN
rs12410866	IGSF8	cis	cerebellum	SCAN
rs12410866	IGSF8	cis	parietal	SCAN
rs12410866	CRP	cis	parietal	SCAN
rs12410866	PEX19	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160088000-160146200	Weak transcription	Spleen	Spleen
2	chr1:160090600-160112600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:160092400-160112200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr1:160094000-160112000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:160094800-160110200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:160097000-160109800	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr1:160097200-160112200	Weak transcription	Brain Germinal Matrix	brain
8	chr1:160098600-160112200	Strong transcription	Fetal Muscle Trunk	muscle
9	chr1:160099800-160109000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:160100000-160114800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:160100600-160112000	Strong transcription	Fetal Muscle Leg	muscle
12	chr1:160102600-160111800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
13	chr1:160103400-160118000	Weak transcription	Right Atrium	heart
14	chr1:160104000-160110200	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:160104200-160110200	Strong transcription	Fetal Stomach	stomach
16	chr1:160105400-160109400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:160106400-160111000	Weak transcription	Brain Anterior Caudate	brain
18	chr1:160106600-160114200	Weak transcription	Adipose Nuclei	Adipose
19	chr1:160106800-160109000	Weak transcription	Aorta	Aorta
20	chr1:160106800-160121600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:160107000-160111400	Weak transcription	Brain Substantia Nigra	brain
22	chr1:160107000-160112200	Strong transcription	Colon Smooth Muscle	Colon
23	chr1:160107000-160112800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:160107200-160109000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:160107200-160109600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:160107400-160109400	Weak transcription	Right Ventricle	heart
27	chr1:160107400-160111400	Weak transcription	Ovary	ovary
28	chr1:160107400-160111800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:160107400-160111800	Strong transcription	Left Ventricle	heart
30	chr1:160107400-160114600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr1:160107600-160109400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:160107600-160110200	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:160107600-160111800	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:160107600-160121400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr1:160108000-160111600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:160108200-160109000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:160108600-160112800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:160108600-160113000	Strong transcription	Stomach Smooth Muscle	stomach
39	chr1:160108800-160112200	Strong transcription	HSMMtube	muscle

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